Interpretive Summary: Stripe rust is one of the most destructive diseases of wheat worldwide. In spite of its agricultural importance, the genomics and genetics of the pathogen are poorly characterized. The pathogen transcripts from spores and germinated spores have been examined previously, but little is known about genes expressed during host infection. Some genes involved in pathogenicity or specific virulence/avirulence in other rust fungi have been found to be specifically expressed in haustoria, special structures of the rust fungus. The objectives of this study were to generate a cDNA library and characterize genes in haustoria of the stripe rust pathogen. A total of 5,126 expressed sequence tags were generated from haustoria, of which 1,134 unique genes were obtained. Approximately 9% and 25% of the genes were homologous to proteins with known function and hypothetical proteins, respectively. The remaining 66% of the unique sequences had no significant similarity in the GenBank. Fourteen genes were predicted to be proteins secreted from haustoria. Analysis of nine genes, including five secreted protein genes revealed expression changes in different developmental and infection stages of the pathogen. This is the first report of haustorial genes for the stripe rust pathogen and the library will be useful for cloning and characterizing pathogenicity genes of the pathogen.

Technical Abstract:
Background: Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most
destructive diseases of wheat (Triticum aestivum L.) worldwide. In spite of its agricultural
importance, the genomics and genetics of the pathogen are poorly characterized. Pst transcripts from urediniospores and germinated urediniospores have been examined previously, but little is known about genes expressed during host infection. Some genes involved in virulence in other rust fungi have been found to be specifically expressed in haustoria. Therefore, the objective of this study was to generate a cDNA library to characterize genes expressed in haustoria of Pst.
Results: A total of 5,126 EST sequences of high quality were generated from haustoria of Pst, from which 287 contigs and 847 singletons were derived. Approximately 10% and 26% of the 1,134 unique sequences were homologous to proteins with known functions and hypothetical proteins, respectively. The remaining 64% of the unique sequences had no significant similarities in GenBank. Fifteen genes were predicted to be proteins secreted from Pst haustoria. Analysis of ten genes, including six secreted protein genes, using quantitative RT-PCR revealed changes in transcript levels in different developmental and infection stages of the pathogen.
Conclusions: The haustorial cDNA library was useful in identifying genes of the stripe rust fungus expressed during the infection process. From the library, we identified 15 genes encoding putative secreted proteins and six genes induced during the infection process. These genes are candidates for further studies to determine their functions in wheat-Pst interactions.